[{"das_tickbox":"1","_id":"17132","quality_controlled":"1","date_published":"2021-05-14T00:00:00Z","article_number":"e1008615","extern":"1","doi":"10.1371/journal.pcbi.1008615","publisher":"Public Library of Science","article_processing_charge":"No","publication_identifier":{"issn":["1553-7358"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"What we can and what we cannot see with extracellular multielectrodes","day":"14","date_created":"2024-06-11T14:43:37Z","oa_version":"Published Version","publication":"PLOS Computational Biology","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1371/journal.pcbi.1008615","open_access":"1"}],"abstract":[{"text":"<jats:p>Extracellular recording is an accessible technique used in animals and humans to study the brain physiology and pathology. As the number of recording channels and their density grows it is natural to ask how much improvement the additional channels bring in and how we can optimally use the new capabilities for monitoring the brain. Here we show that for any given distribution of electrodes we can establish exactly what information about current sources in the brain can be recovered and what information is strictly unobservable. We demonstrate this in the general setting of previously proposed kernel Current Source Density method and illustrate it with simplified examples as well as using evoked potentials from the barrel cortex obtained with a Neuropixels probe and with compatible model data. We show that with conceptual separation of the estimation space from experimental setup one can recover sources not accessible to standard methods.</jats:p>","lang":"eng"}],"status":"public","has_accepted_license":"1","article_type":"original","citation":{"mla":"Chintaluri, Chaitanya, et al. “What We Can and What We Cannot See with Extracellular Multielectrodes.” <i>PLOS Computational Biology</i>, vol. 17, no. 5, e1008615, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008615\">10.1371/journal.pcbi.1008615</a>.","short":"C. Chintaluri, M. Bejtka, W. Średniawa, M. Czerwiński, J.M. Dzik, J. Jędrzejewska-Szmek, K. Kondrakiewicz, E. Kublik, D.K. Wójcik, PLOS Computational Biology 17 (2021).","apa":"Chintaluri, C., Bejtka, M., Średniawa, W., Czerwiński, M., Dzik, J. M., Jędrzejewska-Szmek, J., … Wójcik, D. K. (2021). What we can and what we cannot see with extracellular multielectrodes. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1008615\">https://doi.org/10.1371/journal.pcbi.1008615</a>","ama":"Chintaluri C, Bejtka M, Średniawa W, et al. What we can and what we cannot see with extracellular multielectrodes. <i>PLOS Computational Biology</i>. 2021;17(5). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008615\">10.1371/journal.pcbi.1008615</a>","ieee":"C. Chintaluri <i>et al.</i>, “What we can and what we cannot see with extracellular multielectrodes,” <i>PLOS Computational Biology</i>, vol. 17, no. 5. Public Library of Science, 2021.","ista":"Chintaluri C, Bejtka M, Średniawa W, Czerwiński M, Dzik JM, Jędrzejewska-Szmek J, Kondrakiewicz K, Kublik E, Wójcik DK. 2021. What we can and what we cannot see with extracellular multielectrodes. PLOS Computational Biology. 17(5), e1008615.","chicago":"Chintaluri, Chaitanya, Marta Bejtka, Władysław Średniawa, Michał Czerwiński, Jakub M. Dzik, Joanna Jędrzejewska-Szmek, Kacper Kondrakiewicz, Ewa Kublik, and Daniel K. Wójcik. “What We Can and What We Cannot See with Extracellular Multielectrodes.” <i>PLOS Computational Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pcbi.1008615\">https://doi.org/10.1371/journal.pcbi.1008615</a>."},"language":[{"iso":"eng"}],"intvolume":"        17","date_updated":"2026-07-13T12:31:04Z","author":[{"last_name":"Chintaluri","first_name":"Chaitanya","orcid":"0000-0003-4252-1608","id":"BA06AFEE-A4BA-11EA-AE5C-14673DDC885E","full_name":"Chintaluri, Chaitanya"},{"first_name":"Marta","last_name":"Bejtka","full_name":"Bejtka, Marta"},{"full_name":"Średniawa, Władysław","first_name":"Władysław","last_name":"Średniawa"},{"last_name":"Czerwiński","first_name":"Michał","full_name":"Czerwiński, Michał"},{"first_name":"Jakub M.","last_name":"Dzik","full_name":"Dzik, Jakub M."},{"full_name":"Jędrzejewska-Szmek, Joanna","last_name":"Jędrzejewska-Szmek","first_name":"Joanna"},{"last_name":"Kondrakiewicz","first_name":"Kacper","full_name":"Kondrakiewicz, Kacper"},{"last_name":"Kublik","first_name":"Ewa","full_name":"Kublik, Ewa"},{"last_name":"Wójcik","first_name":"Daniel K.","full_name":"Wójcik, Daniel K."}],"year":"2021","publication_status":"published","issue":"5","volume":17,"month":"05"},{"author":[{"full_name":"Wigderson, Yuval","id":"2d0023a0-1567-11f0-833d-d5c1e476d4b5","last_name":"Wigderson","first_name":"Yuval"}],"page":"2371-2374","publication_status":"published","year":"2021","month":"06","issue":"6","volume":149,"abstract":[{"lang":"eng","text":"A recent breakthrough of Conlon and Ferber yielded an exponential improvement on the lower bounds for multicolor diagonal Ramsey numbers. In this note, we modify their construction and obtain improved bounds for more than three colors."}],"status":"public","external_id":{"unknown":["2009.12020"]},"oa_version":"Preprint","publication":"Proceedings of the American Mathematical Society","date_created":"2026-06-29T10:55:23Z","scopus_import":"1","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2009.12020"}],"article_type":"original","citation":{"apa":"Wigderson, Y. (2021). An improved lower bound on multicolor Ramsey numbers. <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/proc/15447\">https://doi.org/10.1090/proc/15447</a>","ista":"Wigderson Y. 2021. An improved lower bound on multicolor Ramsey numbers. Proceedings of the American Mathematical Society. 149(6), 2371–2374.","ama":"Wigderson Y. An improved lower bound on multicolor Ramsey numbers. <i>Proceedings of the American Mathematical Society</i>. 2021;149(6):2371-2374. doi:<a href=\"https://doi.org/10.1090/proc/15447\">10.1090/proc/15447</a>","ieee":"Y. Wigderson, “An improved lower bound on multicolor Ramsey numbers,” <i>Proceedings of the American Mathematical Society</i>, vol. 149, no. 6. American Mathematical Society, pp. 2371–2374, 2021.","mla":"Wigderson, Yuval. “An Improved Lower Bound on Multicolor Ramsey Numbers.” <i>Proceedings of the American Mathematical Society</i>, vol. 149, no. 6, American Mathematical Society, 2021, pp. 2371–74, doi:<a href=\"https://doi.org/10.1090/proc/15447\">10.1090/proc/15447</a>.","short":"Y. Wigderson, Proceedings of the American Mathematical Society 149 (2021) 2371–2374.","chicago":"Wigderson, Yuval. “An Improved Lower Bound on Multicolor Ramsey Numbers.” <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society, 2021. <a href=\"https://doi.org/10.1090/proc/15447\">https://doi.org/10.1090/proc/15447</a>."},"language":[{"iso":"eng"}],"date_updated":"2026-07-14T08:42:59Z","intvolume":"       149","OA_place":"repository","OA_type":"green","publication_identifier":{"eissn":["1088-6826"],"issn":["0002-9939"]},"article_processing_charge":"No","oa":1,"title":"An improved lower bound on multicolor Ramsey numbers","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","_id":"22169","quality_controlled":"1","date_published":"2021-06-01T00:00:00Z","extern":"1","publisher":"American Mathematical Society","doi":"10.1090/proc/15447"},{"OA_type":"green","arxiv":1,"date_updated":"2026-07-14T09:02:39Z","intvolume":"        58","OA_place":"repository","language":[{"iso":"eng"}],"article_type":"original","citation":{"chicago":"Wigderson, Avi, and Yuval Wigderson. “The Uncertainty Principle: Variations on a Theme.” <i>Bulletin of the American Mathematical Society</i>. American Mathematical Society, 2021. <a href=\"https://doi.org/10.1090/bull/1715\">https://doi.org/10.1090/bull/1715</a>.","short":"A. Wigderson, Y. Wigderson, Bulletin of the American Mathematical Society 58 (2021) 225–261.","mla":"Wigderson, Avi, and Yuval Wigderson. “The Uncertainty Principle: Variations on a Theme.” <i>Bulletin of the American Mathematical Society</i>, vol. 58, no. 2, American Mathematical Society, 2021, pp. 225–61, doi:<a href=\"https://doi.org/10.1090/bull/1715\">10.1090/bull/1715</a>.","ama":"Wigderson A, Wigderson Y. The uncertainty principle: Variations on a theme. <i>Bulletin of the American Mathematical Society</i>. 2021;58(2):225-261. doi:<a href=\"https://doi.org/10.1090/bull/1715\">10.1090/bull/1715</a>","ista":"Wigderson A, Wigderson Y. 2021. The uncertainty principle: Variations on a theme. Bulletin of the American Mathematical Society. 58(2), 225–261.","ieee":"A. Wigderson and Y. Wigderson, “The uncertainty principle: Variations on a theme,” <i>Bulletin of the American Mathematical Society</i>, vol. 58, no. 2. American Mathematical Society, pp. 225–261, 2021.","apa":"Wigderson, A., &#38; Wigderson, Y. (2021). The uncertainty principle: Variations on a theme. <i>Bulletin of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/bull/1715\">https://doi.org/10.1090/bull/1715</a>"},"external_id":{"arxiv":["2006.11206"]},"status":"public","abstract":[{"lang":"eng","text":"We show how a number of well-known uncertainty principles for the Fourier transform, such as the Heisenberg uncertainty principle, the Donoho–Stark uncertainty principle, and Meshulam’s nonabelian uncertainty principle, have little to do with the structure of the Fourier transform itself. Rather, all of these results follow from very weak properties of the Fourier transform (shared by numerous linear operators), namely that it is bounded as an operator  L1 → L∞, and that it is unitary. Using a single, simple proof template, and only these (or weaker) properties, we obtain some new proofs and many generalizations of these basic uncertainty principles, to new operators and to new settings, in a completely unified way. Together with our general overview, this paper can also serve as a survey of the many facets of the phenomena known as uncertainty principles."}],"mathsc":["81S07","43A25","20C15","94A12"],"type":"journal_article","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2006.11206","open_access":"1"}],"date_created":"2026-06-29T10:57:49Z","publication":"Bulletin of the American Mathematical Society","scopus_import":"1","oa_version":"Preprint","month":"01","volume":58,"issue":"2","publication_status":"published","year":"2021","page":"225-261","author":[{"last_name":"Wigderson","first_name":"Avi","full_name":"Wigderson, Avi"},{"id":"2d0023a0-1567-11f0-833d-d5c1e476d4b5","full_name":"Wigderson, Yuval","first_name":"Yuval","last_name":"Wigderson"}],"publisher":"American Mathematical Society","doi":"10.1090/bull/1715","extern":"1","date_published":"2021-01-04T00:00:00Z","_id":"22175","quality_controlled":"1","day":"04","title":"The uncertainty principle: Variations on a theme","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1088-9485"],"issn":["0273-0979"]},"article_processing_charge":"No"},{"has_accepted_license":"1","external_id":{"pmid":["35098222"]},"status":"public","abstract":[{"text":"Phase separation is a ubiquitous process and finds applications in a variety of biological, organic, and inorganic systems. Nature has evolved the ability to control phase separation to both regulate cellular processes and make composite materials with outstanding mechanical and optical properties. Striking examples of the latter are the vibrant blue and green feathers of many bird species, which are thought to result from an exquisite control of the size and spatial correlations of their phase-separated microstructures. By contrast, it is much harder for material scientists to arrest and control phase separation in synthetic materials with such a high level of precision at these length scales. In this Perspective, we briefly review some established methods to control liquid–liquid phase separation processes and then highlight the emergence of a promising arrest method based on phase separation in an elastic polymer network. Finally, we discuss upcoming challenges and opportunities for fabricating microstructured materials via mechanically controlled phase separation.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/jacsau.1c00443"}],"type":"journal_article","publication":"JACS Au","oa_version":"Published Version","scopus_import":"1","date_created":"2026-06-30T06:30:18Z","language":[{"iso":"eng"}],"DOAJ_listed":"1","article_type":"original","citation":{"chicago":"Fernández-Rico, Carla, Tianqi Sai, Alba Sicher, Robert W. Style, and Eric R. Dufresne. “Putting the Squeeze on Phase Separation.” <i>JACS Au</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/jacsau.1c00443\">https://doi.org/10.1021/jacsau.1c00443</a>.","ieee":"C. Fernández-Rico, T. Sai, A. Sicher, R. W. Style, and E. R. Dufresne, “Putting the squeeze on phase separation,” <i>JACS Au</i>, vol. 2, no. 1. American Chemical Society, pp. 66–73, 2021.","ista":"Fernández-Rico C, Sai T, Sicher A, Style RW, Dufresne ER. 2021. Putting the squeeze on phase separation. JACS Au. 2(1), 66–73.","ama":"Fernández-Rico C, Sai T, Sicher A, Style RW, Dufresne ER. Putting the squeeze on phase separation. <i>JACS Au</i>. 2021;2(1):66-73. doi:<a href=\"https://doi.org/10.1021/jacsau.1c00443\">10.1021/jacsau.1c00443</a>","apa":"Fernández-Rico, C., Sai, T., Sicher, A., Style, R. W., &#38; Dufresne, E. R. (2021). Putting the squeeze on phase separation. <i>JACS Au</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacsau.1c00443\">https://doi.org/10.1021/jacsau.1c00443</a>","short":"C. Fernández-Rico, T. Sai, A. Sicher, R.W. Style, E.R. Dufresne, JACS Au 2 (2021) 66–73.","mla":"Fernández-Rico, Carla, et al. “Putting the Squeeze on Phase Separation.” <i>JACS Au</i>, vol. 2, no. 1, American Chemical Society, 2021, pp. 66–73, doi:<a href=\"https://doi.org/10.1021/jacsau.1c00443\">10.1021/jacsau.1c00443</a>."},"ddc":["540"],"date_updated":"2026-07-15T05:55:35Z","OA_place":"publisher","intvolume":"         2","OA_type":"gold","author":[{"full_name":"Fernández-Rico, Carla","id":"492def71-6250-11f0-b278-d41dbd241b62","last_name":"Fernández-Rico","first_name":"Carla"},{"full_name":"Sai, Tianqi","last_name":"Sai","first_name":"Tianqi"},{"full_name":"Sicher, Alba","first_name":"Alba","last_name":"Sicher"},{"full_name":"Style, Robert W.","last_name":"Style","first_name":"Robert W."},{"first_name":"Eric R.","last_name":"Dufresne","full_name":"Dufresne, Eric R."}],"page":"66-73","pmid":1,"publication_status":"published","year":"2021","month":"12","volume":2,"issue":"1","_id":"22207","date_published":"2021-12-10T00:00:00Z","quality_controlled":"1","extern":"1","publisher":"American Chemical Society","doi":"10.1021/jacsau.1c00443","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"publication_identifier":{"eissn":["2691-3704"]},"article_processing_charge":"No","title":"Putting the squeeze on phase separation","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","keyword":["phase separation","arrest","bird feathers","elasticity","polymer networks","microstructured materials"],"day":"10"},{"month":"08","issue":"33","volume":118,"publication_status":"published","year":"2021","pmid":1,"author":[{"id":"492def71-6250-11f0-b278-d41dbd241b62","full_name":"Fernández-Rico, Carla","last_name":"Fernández-Rico","first_name":"Carla"},{"first_name":"Roel P. A.","last_name":"Dullens","full_name":"Dullens, Roel P. A."}],"OA_type":"hybrid","date_updated":"2026-07-15T07:02:38Z","ddc":["540"],"OA_place":"publisher","intvolume":"       118","article_type":"original","citation":{"chicago":"Fernández-Rico, Carla, and Roel P. A. Dullens. “Hierarchical Self-Assembly of Polydisperse Colloidal Bananas into a Two-Dimensional Vortex Phase.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2107241118\">https://doi.org/10.1073/pnas.2107241118</a>.","ama":"Fernández-Rico C, Dullens RPA. Hierarchical self-assembly of polydisperse colloidal bananas into a two-dimensional vortex phase. <i>Proceedings of the National Academy of Sciences</i>. 2021;118(33). doi:<a href=\"https://doi.org/10.1073/pnas.2107241118\">10.1073/pnas.2107241118</a>","ieee":"C. Fernández-Rico and R. P. A. Dullens, “Hierarchical self-assembly of polydisperse colloidal bananas into a two-dimensional vortex phase,” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 33. National Academy of Sciences, 2021.","ista":"Fernández-Rico C, Dullens RPA. 2021. Hierarchical self-assembly of polydisperse colloidal bananas into a two-dimensional vortex phase. Proceedings of the National Academy of Sciences. 118(33), e2107241118.","apa":"Fernández-Rico, C., &#38; Dullens, R. P. A. (2021). Hierarchical self-assembly of polydisperse colloidal bananas into a two-dimensional vortex phase. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2107241118\">https://doi.org/10.1073/pnas.2107241118</a>","short":"C. Fernández-Rico, R.P.A. Dullens, Proceedings of the National Academy of Sciences 118 (2021).","mla":"Fernández-Rico, Carla, and Roel P. A. Dullens. “Hierarchical Self-Assembly of Polydisperse Colloidal Bananas into a Two-Dimensional Vortex Phase.” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 33, e2107241118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2107241118\">10.1073/pnas.2107241118</a>."},"language":[{"iso":"eng"}],"abstract":[{"text":"Hierarchically self-assembled materials—structures with order at multiple length scales—can be found everywhere. Examples range from collagen structures in human bones to engineered photonic materials. These structures usually assemble from monodisperse microscopic building blocks that interact via complex directional interactions. In this work, we show that hierarchical materials can, in fact, also be assembled from polydisperse building blocks and by entropic interactions alone. Our simple yet powerful assembly mechanism opens up avenues toward rationally exploiting the often undesired polydispersity of colloidal building blocks for programming entropy-driven self-assembly of hierarchical materials.","lang":"eng"}],"status":"public","has_accepted_license":"1","external_id":{"pmid":["34389681"]},"oa_version":"Published Version","publication":"Proceedings of the National Academy of Sciences","date_created":"2026-06-30T06:31:50Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.2107241118"}],"type":"journal_article","day":"13","oa":1,"title":"Hierarchical self-assembly of polydisperse colloidal bananas into a two-dimensional vortex phase","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"article_processing_charge":"No","publisher":"National Academy of Sciences","doi":"10.1073/pnas.2107241118","extern":"1","article_number":"e2107241118","_id":"22211","date_published":"2021-08-13T00:00:00Z","quality_controlled":"1"},{"OA_type":"hybrid","OA_place":"publisher","intvolume":"        37","date_updated":"2026-07-15T07:48:42Z","ddc":["540"],"article_type":"original","citation":{"apa":"Fernández-Rico, C., Urbach, J. S., &#38; Dullens, R. P. A. (2021). Synthesis of rough colloidal SU-8 rods and bananas via nanoprecipitation. <i>Langmuir</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.langmuir.0c03361\">https://doi.org/10.1021/acs.langmuir.0c03361</a>","ista":"Fernández-Rico C, Urbach JS, Dullens RPA. 2021. Synthesis of rough colloidal SU-8 rods and bananas via nanoprecipitation. Langmuir. 37(9), 2900–2906.","ieee":"C. Fernández-Rico, J. S. Urbach, and R. P. A. Dullens, “Synthesis of rough colloidal SU-8 rods and bananas via nanoprecipitation,” <i>Langmuir</i>, vol. 37, no. 9. American Chemical Society, pp. 2900–2906, 2021.","ama":"Fernández-Rico C, Urbach JS, Dullens RPA. Synthesis of rough colloidal SU-8 rods and bananas via nanoprecipitation. <i>Langmuir</i>. 2021;37(9):2900-2906. doi:<a href=\"https://doi.org/10.1021/acs.langmuir.0c03361\">10.1021/acs.langmuir.0c03361</a>","mla":"Fernández-Rico, Carla, et al. “Synthesis of Rough Colloidal SU-8 Rods and Bananas via Nanoprecipitation.” <i>Langmuir</i>, vol. 37, no. 9, American Chemical Society, 2021, pp. 2900–06, doi:<a href=\"https://doi.org/10.1021/acs.langmuir.0c03361\">10.1021/acs.langmuir.0c03361</a>.","short":"C. Fernández-Rico, J.S. Urbach, R.P.A. Dullens, Langmuir 37 (2021) 2900–2906.","chicago":"Fernández-Rico, Carla, Jeffrey S. Urbach, and Roel P. A. Dullens. “Synthesis of Rough Colloidal SU-8 Rods and Bananas via Nanoprecipitation.” <i>Langmuir</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/acs.langmuir.0c03361\">https://doi.org/10.1021/acs.langmuir.0c03361</a>."},"language":[{"iso":"eng"}],"scopus_import":"1","oa_version":"Published Version","publication":"Langmuir","date_created":"2026-06-30T06:36:01Z","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acs.langmuir.0c03361"}],"abstract":[{"text":"Surface roughness plays an important role in determining the mechanical properties, wettability, and self-assembly in colloidal systems. In this work, we develop a simple and fast method to produce rough colloidal SU-8 rods, bananas, and spheres, via the nanoprecipitation of SU-8 in water. During this process, SU-8 nanospheres are absorbed onto the surface of the colloidal SU-8 particles and then cross-linked using UV-light. The size of the spherical asperities and the asperity density are controlled by the concentration of SU-8 used during the nanoprecipitation reaction. Fluorescent labeling of the rough SU-8 colloidal particles allows for their confocal imaging, which demonstrates their stability at high packing fractions. With these newly developed rough particles, we provide a colloidal model system that allows for studies addressing the impact of surface roughness on materials composed of anisotropic particles.","lang":"eng"}],"external_id":{"pmid":["33635671"]},"has_accepted_license":"1","status":"public","issue":"9","volume":37,"month":"02","year":"2021","publication_status":"published","pmid":1,"page":"2900-2906","author":[{"full_name":"Fernández-Rico, Carla","id":"492def71-6250-11f0-b278-d41dbd241b62","last_name":"Fernández-Rico","first_name":"Carla"},{"last_name":"Urbach","first_name":"Jeffrey S.","full_name":"Urbach, Jeffrey S."},{"first_name":"Roel P. A.","last_name":"Dullens","full_name":"Dullens, Roel P. A."}],"doi":"10.1021/acs.langmuir.0c03361","publisher":"American Chemical Society","extern":"1","_id":"22217","quality_controlled":"1","date_published":"2021-02-26T00:00:00Z","day":"26","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Synthesis of rough colloidal SU-8 rods and bananas via nanoprecipitation","article_processing_charge":"No","publication_identifier":{"issn":["0743-7463"],"eissn":["1520-5827"]},"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"}},{"external_id":{"isi":["000636121800001"],"pmid":["33634751"]},"status":"public","abstract":[{"lang":"eng","text":"In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field. "}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1080/15548627.2020.1797280"}],"type":"journal_article","scopus_import":"1","oa_version":"Published Version","publication":"Autophagy","date_created":"2021-03-28T22:01:44Z","language":[{"iso":"eng"}],"citation":{"chicago":"Klionsky, Daniel J., Amal Kamal Abdel-Aziz, Sara Abdelfatah, Mahmoud Abdellatif, Asghar Abdoli, Steffen Abel, Hagai Abeliovich, et al. “Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy (4th Edition).” <i>Autophagy</i>. Taylor &#38; Francis, 2021. <a href=\"https://doi.org/10.1080/15548627.2020.1797280\">https://doi.org/10.1080/15548627.2020.1797280</a>.","short":"D.J. Klionsky, A.K. Abdel-Aziz, S. Abdelfatah, M. Abdellatif, A. Abdoli, S. Abel, H. Abeliovich, M.H. Abildgaard, Y.P. Abudu, A. Acevedo-Arozena, I.E. Adamopoulos, K. Adeli, T.E. Adolph, A. Adornetto, E. Aflaki, G. Agam, A. Agarwal, B.B. Aggarwal, M. Agnello, P. Agostinis, J.N. Agrewala, A. Agrotis, P.V. 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J., Abdel-Aziz, A. K., Abdelfatah, S., Abdellatif, M., Abdoli, A., Abel, S., … Tong, C. K. (2021). Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). <i>Autophagy</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/15548627.2020.1797280\">https://doi.org/10.1080/15548627.2020.1797280</a>"},"article_type":"review","ddc":["580","570"],"date_updated":"2026-07-28T12:37:19Z","intvolume":"        17","OA_type":"free access","author":[{"full_name":"Klionsky, Daniel J.","first_name":"Daniel J.","last_name":"Klionsky"},{"first_name":"Amal Kamal","last_name":"Abdel-Aziz","full_name":"Abdel-Aziz, Amal Kamal"},{"full_name":"Abdelfatah, Sara","first_name":"Sara","last_name":"Abdelfatah"},{"first_name":"Mahmoud","last_name":"Abdellatif","full_name":"Abdellatif, Mahmoud"},{"full_name":"Abdoli, Asghar","first_name":"Asghar","last_name":"Abdoli"},{"full_name":"Abel, Steffen","first_name":"Steffen","last_name":"Abel"},{"last_name":"Abeliovich","first_name":"Hagai","full_name":"Abeliovich, Hagai"},{"last_name":"Abildgaard","first_name":"Marie H.","full_name":"Abildgaard, Marie H."},{"full_name":"Abudu, Yakubu Princely","last_name":"Abudu","first_name":"Yakubu Princely"},{"full_name":"Acevedo-Arozena, Abraham","last_name":"Acevedo-Arozena","first_name":"Abraham"},{"full_name":"Adamopoulos, Iannis E.","last_name":"Adamopoulos","first_name":"Iannis E."},{"full_name":"Adeli, Khosrow","last_name":"Adeli","first_name":"Khosrow"},{"full_name":"Adolph, Timon E.","last_name":"Adolph","first_name":"Timon E."},{"full_name":"Adornetto, Annagrazia","last_name":"Adornetto","first_name":"Annagrazia"},{"last_name":"Aflaki","first_name":"Elma","full_name":"Aflaki, Elma"},{"first_name":"Galila","last_name":"Agam","full_name":"Agam, Galila"},{"full_name":"Agarwal, Anupam","last_name":"Agarwal","first_name":"Anupam"},{"full_name":"Aggarwal, Bharat B.","last_name":"Aggarwal","first_name":"Bharat B."},{"last_name":"Agnello","first_name":"Maria","full_name":"Agnello, Maria"},{"first_name":"Patrizia","last_name":"Agostinis","full_name":"Agostinis, Patrizia"},{"full_name":"Agrewala, Javed N.","last_name":"Agrewala","first_name":"Javed N."},{"first_name":"Alexander","last_name":"Agrotis","full_name":"Agrotis, Alexander"},{"full_name":"Aguilar, Patricia V.","last_name":"Aguilar","first_name":"Patricia V."},{"full_name":"Ahmad, S. 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M.","last_name":"Zimmermann","full_name":"Zimmermann, Christine M."},{"full_name":"Ziviani, Elena","first_name":"Elena","last_name":"Ziviani"},{"first_name":"Teresa","last_name":"Zoladek","full_name":"Zoladek, Teresa"},{"full_name":"Zong, Wei Xing","first_name":"Wei Xing","last_name":"Zong"},{"first_name":"Dmitry B.","last_name":"Zorov","full_name":"Zorov, Dmitry B."},{"first_name":"Antonio","last_name":"Zorzano","full_name":"Zorzano, Antonio"},{"full_name":"Zou, Weiping","first_name":"Weiping","last_name":"Zou"},{"first_name":"Zhen","last_name":"Zou","full_name":"Zou, Zhen"},{"full_name":"Zou, Zhengzhi","first_name":"Zhengzhi","last_name":"Zou"},{"last_name":"Zuryn","first_name":"Steven","full_name":"Zuryn, Steven"},{"full_name":"Zwerschke, Werner","first_name":"Werner","last_name":"Zwerschke"},{"full_name":"Brand-Saberi, Beate","first_name":"Beate","last_name":"Brand-Saberi"},{"full_name":"Dong, X. Charlie","first_name":"X. Charlie","last_name":"Dong"},{"full_name":"Kenchappa, Chandra Shekar","last_name":"Kenchappa","first_name":"Chandra Shekar"},{"full_name":"Li, Zuguo","last_name":"Li","first_name":"Zuguo"},{"first_name":"Yong","last_name":"Lin","full_name":"Lin, Yong"},{"last_name":"Oshima","first_name":"Shigeru","full_name":"Oshima, Shigeru"},{"full_name":"Rong, Yueguang","last_name":"Rong","first_name":"Yueguang"},{"full_name":"Sluimer, Judith C.","first_name":"Judith C.","last_name":"Sluimer"},{"full_name":"Stallings, Christina L.","first_name":"Christina L.","last_name":"Stallings"},{"first_name":"Chun Kit","last_name":"Tong","full_name":"Tong, Chun Kit"}],"page":"1-382","pmid":1,"publication_status":"published","year":"2021","month":"02","volume":17,"issue":"1","date_published":"2021-02-08T00:00:00Z","_id":"9298","quality_controlled":"1","publisher":"Taylor & Francis","doi":"10.1080/15548627.2020.1797280","isi":1,"acknowledgement":"This work was supported by the National Institute of General Medical Sciences [GM131919]. Due to space and other limitations, it is not possible to include all other sources of financial support.","publication_identifier":{"issn":["1554-8627"],"eissn":["1554-8635"]},"article_processing_charge":"No","title":"Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"},{"_id":"CaHe"}],"day":"08"},{"year":"2021","publication_status":"published","volume":217,"issue":"2","month":"02","author":[{"orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"pmid":1,"intvolume":"       217","OA_place":"publisher","ddc":["570"],"date_updated":"2026-07-28T12:39:03Z","OA_type":"free access","project":[{"call_identifier":"FWF","_id":"2662AADE-B435-11E9-9278-68D0E5697425","name":"Sex chromosomes and species barriers","grant_number":"M02463"}],"type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1093/genetics/iyaa025","open_access":"1"}],"corr_author":"1","publication":"Genetics","scopus_import":"1","oa_version":"Published Version","date_created":"2021-02-18T14:41:30Z","external_id":{"pmid":["33724409"],"isi":["000637218100005"]},"status":"public","abstract":[{"lang":"eng","text":"Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems."}],"language":[{"iso":"eng"}],"article_type":"original","citation":{"chicago":"Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” <i>Genetics</i>. Genetics Society of America, 2021. <a href=\"https://doi.org/10.1093/genetics/iyaa025\">https://doi.org/10.1093/genetics/iyaa025</a>.","ieee":"C. Fraisse and H. Sachdeva, “The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes,” <i>Genetics</i>, vol. 217, no. 2. Genetics Society of America, 2021.","ista":"Fraisse C, Sachdeva H. 2021. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. 217(2), iyaa025.","ama":"Fraisse C, Sachdeva H. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. <i>Genetics</i>. 2021;217(2). doi:<a href=\"https://doi.org/10.1093/genetics/iyaa025\">10.1093/genetics/iyaa025</a>","apa":"Fraisse, C., &#38; Sachdeva, H. (2021). The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1093/genetics/iyaa025\">https://doi.org/10.1093/genetics/iyaa025</a>","short":"C. Fraisse, H. Sachdeva, Genetics 217 (2021).","mla":"Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” <i>Genetics</i>, vol. 217, no. 2, iyaa025, Genetics Society of America, 2021, doi:<a href=\"https://doi.org/10.1093/genetics/iyaa025\">10.1093/genetics/iyaa025</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes","oa":1,"day":"01","department":[{"_id":"NiBa"}],"article_processing_charge":"No","publication_identifier":{"issn":["1943-2631"]},"doi":"10.1093/genetics/iyaa025","isi":1,"acknowledgement":"The computations were performed with the IST Austria High-Performance Computing (HPC) Cluster and the Institut Français de Bioinformatique (IFB) Core Cluster. We are grateful to Nick Barton and Beatriz Vicoso for critical comments on the model and the manuscript. We also thank Brian Charlesworth, Stuart Baird, and an anonymous reviewer for insightful comments.\r\nC.F. was supported by an Austrian Science Foundation FWF grant (Project M 2463-B29).","publisher":"Genetics Society of America","quality_controlled":"1","_id":"9168","date_published":"2021-02-01T00:00:00Z","article_number":"iyaa025"},{"abstract":[{"lang":"eng","text":"Astrocytes extensively infiltrate the neuropil to regulate critical aspects of synaptic development and function. This process is regulated by transcellular interactions between astrocytes and neurons via cell adhesion molecules. How astrocytes coordinate developmental processes among one another to parse out the synaptic neuropil and form non-overlapping territories is unknown. Here we identify a molecular mechanism regulating astrocyte-astrocyte interactions during development to coordinate astrocyte morphogenesis and gap junction coupling. We show that hepaCAM, a disease-linked, astrocyte-enriched cell adhesion molecule, regulates astrocyte competition for territory and morphological complexity in the developing mouse cortex. Furthermore, conditional deletion of Hepacam from developing astrocytes significantly impairs gap junction coupling between astrocytes and disrupts the balance between synaptic excitation and inhibition. Mutations in HEPACAM cause megalencephalic leukoencephalopathy with subcortical cysts in humans. Therefore, our findings suggest that disruption of astrocyte self-organization mechanisms could be an underlying cause of neural pathology."}],"status":"public","external_id":{"isi":["000692851900010"],"pmid":["34171291"]},"publication":"Neuron","oa_version":"Published Version","scopus_import":"1","date_created":"2021-08-06T09:08:25Z","main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2021.05.025","open_access":"1"}],"type":"journal_article","citation":{"chicago":"Baldwin, Katherine T., Christabel X. Tan, Samuel T. Strader, Changyu Jiang, Justin T. Savage, Xabier Elorza-Vidal, Ximena Contreras, et al. “HepaCAM Controls Astrocyte Self-Organization and Coupling.” <i>Neuron</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.neuron.2021.05.025\">https://doi.org/10.1016/j.neuron.2021.05.025</a>.","mla":"Baldwin, Katherine T., et al. “HepaCAM Controls Astrocyte Self-Organization and Coupling.” <i>Neuron</i>, vol. 109, no. 15, Elsevier, 2021, p. 2427–2442.e10, doi:<a href=\"https://doi.org/10.1016/j.neuron.2021.05.025\">10.1016/j.neuron.2021.05.025</a>.","short":"K.T. Baldwin, C.X. Tan, S.T. Strader, C. Jiang, J.T. Savage, X. Elorza-Vidal, X. Contreras, T. Rülicke, S. Hippenmeyer, R. Estévez, R.-R. Ji, C. Eroglu, Neuron 109 (2021) 2427–2442.e10.","apa":"Baldwin, K. T., Tan, C. X., Strader, S. T., Jiang, C., Savage, J. T., Elorza-Vidal, X., … Eroglu, C. (2021). HepaCAM controls astrocyte self-organization and coupling. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2021.05.025\">https://doi.org/10.1016/j.neuron.2021.05.025</a>","ama":"Baldwin KT, Tan CX, Strader ST, et al. HepaCAM controls astrocyte self-organization and coupling. <i>Neuron</i>. 2021;109(15):2427-2442.e10. doi:<a href=\"https://doi.org/10.1016/j.neuron.2021.05.025\">10.1016/j.neuron.2021.05.025</a>","ieee":"K. T. Baldwin <i>et al.</i>, “HepaCAM controls astrocyte self-organization and coupling,” <i>Neuron</i>, vol. 109, no. 15. Elsevier, p. 2427–2442.e10, 2021.","ista":"Baldwin KT, Tan CX, Strader ST, Jiang C, Savage JT, Elorza-Vidal X, Contreras X, Rülicke T, Hippenmeyer S, Estévez R, Ji R-R, Eroglu C. 2021. HepaCAM controls astrocyte self-organization and coupling. Neuron. 109(15), 2427–2442.e10."},"article_type":"original","ec_funded":1,"language":[{"iso":"eng"}],"date_updated":"2026-07-28T12:30:05Z","ddc":["570"],"intvolume":"       109","OA_place":"publisher","OA_type":"free access","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780"}],"author":[{"full_name":"Baldwin, Katherine T.","last_name":"Baldwin","first_name":"Katherine T."},{"last_name":"Tan","first_name":"Christabel X.","full_name":"Tan, Christabel X."},{"first_name":"Samuel T.","last_name":"Strader","full_name":"Strader, Samuel T."},{"first_name":"Changyu","last_name":"Jiang","full_name":"Jiang, Changyu"},{"full_name":"Savage, Justin T.","first_name":"Justin T.","last_name":"Savage"},{"first_name":"Xabier","last_name":"Elorza-Vidal","full_name":"Elorza-Vidal, Xabier"},{"last_name":"Contreras","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","full_name":"Contreras, Ximena"},{"full_name":"Rülicke, Thomas","last_name":"Rülicke","first_name":"Thomas"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"},{"full_name":"Estévez, Raúl","first_name":"Raúl","last_name":"Estévez"},{"full_name":"Ji, Ru-Rong","first_name":"Ru-Rong","last_name":"Ji"},{"full_name":"Eroglu, Cagla","last_name":"Eroglu","first_name":"Cagla"}],"page":"2427-2442.e10","pmid":1,"publication_status":"published","year":"2021","month":"08","issue":"15","volume":109,"_id":"9793","date_published":"2021-08-04T00:00:00Z","quality_controlled":"1","publisher":"Elsevier","isi":1,"acknowledgement":"This work was supported by the National Institutes of Health (R01 DA047258 and R01 NS102237 to C.E., F32 NS100392 to K.T.B.) and the Holland-Trice Brain Research Award (to C.E.). K.T.B. was supported by postdoctoral fellowships from the Foerster-Bernstein Family and The Hartwell Foundation. The Hippenmeyer lab was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovations program (725780 LinPro) to S.H. R.E. was supported by Ministerio de Ciencia y Tecnología (RTI2018-093493-B-I00). We thank the Duke Light Microscopy Core Facility, the Duke Transgenic Mouse Facility, Dr. U. Schulte for assistance with proteomic experiments, and Dr. D. Silver for critical review of the manuscript. Cartoon elements of figure panels were created using BioRender.com.","doi":"10.1016/j.neuron.2021.05.025","publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"article_processing_charge":"No","oa":1,"title":"HepaCAM controls astrocyte self-organization and coupling","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SiHi"}],"day":"04"},{"date_published":"2021-11-01T00:00:00Z","_id":"10363","quality_controlled":"1","article_number":"gzab025","doi":"10.1093/protein/gzab025","isi":1,"acknowledgement":"This work was supported by funds from the Wyss Institute for Biologically Inspired Engineering and the Boston Biomedical Innovation Center (Pilot Award 112475; Drive Award U54HL119145). J.L., K.M.K., D.R.B., J.C.W. and P.A.S. were supported by the Harvard Medical School Department of Systems Biology. J.C.W. was further supported by the Harvard Medical School Laboratory of Systems Pharmacology. A.V., D.R.B. and P.A.S. were further supported by the Wyss Institute for Biologically Inspired Engineering. N.G.G. was sponsored by the Army Research Office under Grant Number W911NF-17-2-0092. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the Army Research Office or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright notation herein. We sincerely thank Amanda Graveline and the Wyss Institute at Harvard for their scientific support.","publisher":"Oxford University Press","article_processing_charge":"No","publication_identifier":{"eissn":["1741-0134"],"issn":["1741-0126"]},"day":"01","department":[{"_id":"CaGu"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Rational engineering of an erythropoietin fusion protein to treat hypoxia","oa":1,"language":[{"iso":"eng"}],"citation":{"ama":"Lee J, Vernet A, Gruber N, et al. Rational engineering of an erythropoietin fusion protein to treat hypoxia. <i>Protein Engineering, Design and Selection</i>. 2021;34. doi:<a href=\"https://doi.org/10.1093/protein/gzab025\">10.1093/protein/gzab025</a>","ieee":"J. Lee <i>et al.</i>, “Rational engineering of an erythropoietin fusion protein to treat hypoxia,” <i>Protein Engineering, Design and Selection</i>, vol. 34. Oxford University Press, 2021.","ista":"Lee J, Vernet A, Gruber N, Kready KM, Burrill DR, Way JC, Silver PA. 2021. Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. 34, gzab025.","apa":"Lee, J., Vernet, A., Gruber, N., Kready, K. M., Burrill, D. R., Way, J. C., &#38; Silver, P. A. (2021). Rational engineering of an erythropoietin fusion protein to treat hypoxia. <i>Protein Engineering, Design and Selection</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/protein/gzab025\">https://doi.org/10.1093/protein/gzab025</a>","short":"J. Lee, A. Vernet, N. Gruber, K.M. Kready, D.R. Burrill, J.C. Way, P.A. Silver, Protein Engineering, Design and Selection 34 (2021).","mla":"Lee, Jungmin, et al. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.” <i>Protein Engineering, Design and Selection</i>, vol. 34, gzab025, Oxford University Press, 2021, doi:<a href=\"https://doi.org/10.1093/protein/gzab025\">10.1093/protein/gzab025</a>.","chicago":"Lee, Jungmin, Andyna Vernet, Nathalie Gruber, Kasia M. Kready, Devin R. Burrill, Jeffrey C. Way, and Pamela A. Silver. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.” <i>Protein Engineering, Design and Selection</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/protein/gzab025\">https://doi.org/10.1093/protein/gzab025</a>."},"article_type":"original","main_file_link":[{"url":"https://doi.org/10.1093/protein/gzab025","open_access":"1"}],"type":"journal_article","date_created":"2021-11-28T23:01:28Z","oa_version":"Published Version","scopus_import":"1","publication":"Protein Engineering, Design and Selection","status":"public","external_id":{"isi":["000746596900001"],"pmid":["34725710"]},"abstract":[{"lang":"eng","text":"Erythropoietin enhances oxygen delivery and reduces hypoxia-induced cell death, but its pro-thrombotic activity is problematic for use of erythropoietin in treating hypoxia. We constructed a fusion protein that stimulates red blood cell production and neuroprotection without triggering platelet production, a marker for thrombosis. The protein consists of an anti-glycophorin A nanobody and an erythropoietin mutant (L108A). The mutation reduces activation of erythropoietin receptor homodimers that induce erythropoiesis and thrombosis, but maintains the tissue-protective signaling. The binding of the nanobody element to glycophorin A rescues homodimeric erythropoietin receptor activation on red blood cell precursors. In a cell proliferation assay, the fusion protein is active at 10−14 M, allowing an estimate of the number of receptor–ligand complexes needed for signaling. This fusion protein stimulates erythroid cell proliferation in vitro and in mice, and shows neuroprotective activity in vitro. Our erythropoietin fusion protein presents a novel molecule for treating hypoxia."}],"OA_type":"free access","OA_place":"publisher","intvolume":"        34","ddc":["570"],"date_updated":"2026-07-28T12:27:59Z","pmid":1,"author":[{"first_name":"Jungmin","last_name":"Lee","full_name":"Lee, Jungmin"},{"first_name":"Andyna","last_name":"Vernet","full_name":"Vernet, Andyna"},{"first_name":"Nathalie","last_name":"Gruber","full_name":"Gruber, Nathalie","id":"2C9C8316-AA17-11E9-B5C2-8BC2E5697425"},{"full_name":"Kready, Kasia M.","last_name":"Kready","first_name":"Kasia M."},{"full_name":"Burrill, Devin R.","last_name":"Burrill","first_name":"Devin R."},{"full_name":"Way, Jeffrey C.","first_name":"Jeffrey C.","last_name":"Way"},{"full_name":"Silver, Pamela A.","last_name":"Silver","first_name":"Pamela A."}],"volume":34,"month":"11","year":"2021","publication_status":"published"},{"date_updated":"2026-07-28T12:16:17Z","intvolume":"       371","OA_type":"closed access","external_id":{"isi":["000617551600027"],"pmid":["33574201"]},"status":"public","abstract":[{"lang":"eng","text":"Thermoelectric materials are engines that convert heat into an electrical current. Intuitively, the efficiency of this process depends on how many electrons (charge carriers) can move and how easily they do so, how much energy those moving electrons transport, and how easily the temperature gradient is maintained. In terms of material properties, an excellent thermoelectric material requires a high electrical conductivity σ, a high Seebeck coefficient S (a measure of the induced thermoelectric voltage as a function of temperature gradient), and a low thermal conductivity κ. The challenge is that these three properties are strongly interrelated in a conflicting manner (1). On page 722 of this issue, Roychowdhury et al. (2) have found a way to partially break these ties in silver antimony telluride (AgSbTe2) with the addition of cadmium (Cd) cations, which increase the ordering in this inherently disordered thermoelectric material."}],"corr_author":"1","type":"journal_article","date_created":"2022-03-03T09:51:48Z","oa_version":"None","scopus_import":"1","publication":"Science","language":[{"iso":"eng"}],"citation":{"mla":"Liu, Yu, and Maria Ibáñez. “Tidying up the Mess.” <i>Science</i>, vol. 371, no. 6530, American Association for the Advancement of Science, 2021, pp. 678–79, doi:<a href=\"https://doi.org/10.1126/science.abg0886\">10.1126/science.abg0886</a>.","short":"Y. Liu, M. Ibáñez, Science 371 (2021) 678–679.","apa":"Liu, Y., &#38; Ibáñez, M. (2021). Tidying up the mess. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.abg0886\">https://doi.org/10.1126/science.abg0886</a>","ieee":"Y. Liu and M. Ibáñez, “Tidying up the mess,” <i>Science</i>, vol. 371, no. 6530. American Association for the Advancement of Science, pp. 678–679, 2021.","ista":"Liu Y, Ibáñez M. 2021. Tidying up the mess. Science. 371(6530), 678–679.","ama":"Liu Y, Ibáñez M. Tidying up the mess. <i>Science</i>. 2021;371(6530):678-679. doi:<a href=\"https://doi.org/10.1126/science.abg0886\">10.1126/science.abg0886</a>","chicago":"Liu, Yu, and Maria Ibáñez. “Tidying up the Mess.” <i>Science</i>. American Association for the Advancement of Science, 2021. <a href=\"https://doi.org/10.1126/science.abg0886\">https://doi.org/10.1126/science.abg0886</a>."},"article_type":"letter_note","publication_status":"published","year":"2021","month":"02","volume":371,"issue":"6530","author":[{"last_name":"Liu","orcid":"0000-0001-7313-6740","first_name":"Yu","full_name":"Liu, Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843"}],"page":"678-679","pmid":1,"publisher":"American Association for the Advancement of Science","isi":1,"doi":"10.1126/science.abg0886","_id":"10809","date_published":"2021-02-12T00:00:00Z","quality_controlled":"1","title":"Tidying up the mess","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MaIb"}],"day":"12","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"article_processing_charge":"No"},{"article_processing_charge":"No","publication_identifier":{"eissn":["1879-081X"],"issn":["0925-7721"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"title":"Folding polyominoes with holes into a cube","day":"01","department":[{"_id":"HeEd"}],"date_published":"2021-02-01T00:00:00Z","_id":"8317","quality_controlled":"1","article_number":"101700","doi":"10.1016/j.comgeo.2020.101700","isi":1,"acknowledgement":"This research was performed in part at the 33rd Bellairs Winter Workshop on Computational Geometry. We thank all other participants for a fruitful atmosphere. H. Akitaya was supported by NSF CCF-1422311 & 1423615. Z. Masárová was partially funded by Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31.","publisher":"Elsevier","author":[{"full_name":"Aichholzer, Oswin","first_name":"Oswin","last_name":"Aichholzer"},{"full_name":"Akitaya, Hugo A.","first_name":"Hugo A.","last_name":"Akitaya"},{"full_name":"Cheung, Kenneth C.","last_name":"Cheung","first_name":"Kenneth C."},{"full_name":"Demaine, Erik D.","last_name":"Demaine","first_name":"Erik D."},{"last_name":"Demaine","first_name":"Martin L.","full_name":"Demaine, Martin L."},{"first_name":"Sándor P.","last_name":"Fekete","full_name":"Fekete, Sándor P."},{"full_name":"Kleist, Linda","first_name":"Linda","last_name":"Kleist"},{"first_name":"Irina","last_name":"Kostitsyna","full_name":"Kostitsyna, Irina"},{"last_name":"Löffler","first_name":"Maarten","full_name":"Löffler, Maarten"},{"id":"45CFE238-F248-11E8-B48F-1D18A9856A87","full_name":"Masárová, Zuzana","last_name":"Masárová","first_name":"Zuzana","orcid":"0000-0002-6660-1322"},{"full_name":"Mundilova, Klara","first_name":"Klara","last_name":"Mundilova"},{"full_name":"Schmidt, Christiane","first_name":"Christiane","last_name":"Schmidt"}],"year":"2021","publication_status":"published","related_material":{"record":[{"status":"public","id":"6989","relation":"shorter_version"}]},"volume":93,"month":"02","date_created":"2020-08-30T22:01:09Z","publication":"Computational Geometry: Theory and Applications","scopus_import":"1","oa_version":"Preprint","corr_author":"1","type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1910.09917v3","open_access":"1"}],"abstract":[{"lang":"eng","text":"When can a polyomino piece of paper be folded into a unit cube? Prior work studied tree-like polyominoes, but polyominoes with holes remain an intriguing open problem. We present sufficient conditions for a polyomino with one or several holes to fold into a cube, and conditions under which cube folding is impossible. In particular, we show that all but five special “basic” holes guarantee foldability."}],"external_id":{"arxiv":["1910.09917"],"isi":["000579185100004"]},"status":"public","citation":{"ama":"Aichholzer O, Akitaya HA, Cheung KC, et al. Folding polyominoes with holes into a cube. <i>Computational Geometry: Theory and Applications</i>. 2021;93. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2020.101700\">10.1016/j.comgeo.2020.101700</a>","ista":"Aichholzer O, Akitaya HA, Cheung KC, Demaine ED, Demaine ML, Fekete SP, Kleist L, Kostitsyna I, Löffler M, Masárová Z, Mundilova K, Schmidt C. 2021. Folding polyominoes with holes into a cube. Computational Geometry: Theory and Applications. 93, 101700.","ieee":"O. Aichholzer <i>et al.</i>, “Folding polyominoes with holes into a cube,” <i>Computational Geometry: Theory and Applications</i>, vol. 93. Elsevier, 2021.","apa":"Aichholzer, O., Akitaya, H. A., Cheung, K. C., Demaine, E. D., Demaine, M. L., Fekete, S. P., … Schmidt, C. (2021). Folding polyominoes with holes into a cube. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2020.101700\">https://doi.org/10.1016/j.comgeo.2020.101700</a>","short":"O. Aichholzer, H.A. Akitaya, K.C. Cheung, E.D. Demaine, M.L. Demaine, S.P. Fekete, L. Kleist, I. Kostitsyna, M. Löffler, Z. Masárová, K. Mundilova, C. Schmidt, Computational Geometry: Theory and Applications 93 (2021).","mla":"Aichholzer, Oswin, et al. “Folding Polyominoes with Holes into a Cube.” <i>Computational Geometry: Theory and Applications</i>, vol. 93, 101700, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2020.101700\">10.1016/j.comgeo.2020.101700</a>.","chicago":"Aichholzer, Oswin, Hugo A. Akitaya, Kenneth C. Cheung, Erik D. Demaine, Martin L. Demaine, Sándor P. Fekete, Linda Kleist, et al. “Folding Polyominoes with Holes into a Cube.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.comgeo.2020.101700\">https://doi.org/10.1016/j.comgeo.2020.101700</a>."},"article_type":"original","language":[{"iso":"eng"}],"intvolume":"        93","date_updated":"2026-07-28T13:08:48Z","arxiv":1,"project":[{"grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science","call_identifier":"FWF"}]},{"language":[{"iso":"eng"}],"citation":{"mla":"Lombardi, Fabrizio, et al. <i>Quantifying the Coexistence of Neuronal Oscillations and Avalanches</i>. 2108.06686, arXiv, doi:<a href=\"https://doi.org/10.48550/ARXIV.2108.06686\">10.48550/ARXIV.2108.06686</a>.","short":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, (n.d.).","apa":"Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., &#38; De Martino, D. (n.d.). Quantifying the coexistence of neuronal oscillations and avalanches. arXiv. <a href=\"https://doi.org/10.48550/ARXIV.2108.06686\">https://doi.org/10.48550/ARXIV.2108.06686</a>","ieee":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Quantifying the coexistence of neuronal oscillations and avalanches.” arXiv.","ista":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Quantifying the coexistence of neuronal oscillations and avalanches. 2108.06686.","ama":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Quantifying the coexistence of neuronal oscillations and avalanches. doi:<a href=\"https://doi.org/10.48550/ARXIV.2108.06686\">10.48550/ARXIV.2108.06686</a>","chicago":"Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele De Martino. “Quantifying the Coexistence of Neuronal Oscillations and Avalanches.” arXiv, n.d. <a href=\"https://doi.org/10.48550/ARXIV.2108.06686\">https://doi.org/10.48550/ARXIV.2108.06686</a>."},"ec_funded":1,"status":"public","external_id":{"arxiv":["2108.06686"]},"abstract":[{"text":"Brain dynamics display collective phenomena as diverse as neuronal oscillations and avalanches. Oscillations are rhythmic, with fluctuations occurring at a characteristic scale, whereas avalanches are scale-free cascades of neural activity. Here we show that such antithetic features can coexist in a very generic class of adaptive neural networks. In the most simple yet fully microscopic model from this class we make direct contact with human brain resting-state activity recordings via tractable inference of the model's two essential parameters. The inferred model quantitatively captures the dynamics over a broad range of scales, from single sensor fluctuations, collective behaviors of nearly-synchronous extreme events on multiple sensors, to neuronal avalanches unfolding over multiple sensors across multiple time-bins. Importantly, the inferred parameters correlate with model-independent signatures of \"closeness to criticality\", suggesting that the coexistence of scale-specific (neural oscillations) and scale-free (neuronal avalanches) dynamics in brain activity occurs close to a non-equilibrium critical point at the onset of self-sustained oscillations.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2108.06686"}],"type":"preprint","date_created":"2022-03-21T11:41:28Z","oa_version":"Preprint","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","name":"Efficient coding with biophysical realism","grant_number":"P34015"}],"OA_type":"green","arxiv":1,"ddc":["570"],"date_updated":"2026-07-29T06:53:41Z","OA_place":"repository","author":[{"id":"A057D288-3E88-11E9-986D-0CF4E5697425","full_name":"Lombardi, Fabrizio","first_name":"Fabrizio","orcid":"0000-0003-2623-5249","last_name":"Lombardi"},{"full_name":"Pepic, Selver","id":"F93245C4-C3CA-11E9-B4F0-C6F4E5697425","first_name":"Selver","last_name":"Pepic"},{"first_name":"Oren","last_name":"Shriki","full_name":"Shriki, Oren"},{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","first_name":"Gašper","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Daniele","last_name":"De Martino","full_name":"De Martino, Daniele"}],"month":"08","related_material":{"record":[{"relation":"later_version","id":"12762","status":"public"}]},"publication_status":"submitted","year":"2021","article_number":"2108.06686","_id":"10912","date_published":"2021-08-17T00:00:00Z","publisher":"arXiv","acknowledgement":"FL acknowledges support from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411. GT\r\nacknowledges the support of the Austrian Science Fund (FWF) under Stand-Alone Grant\r\nNo. P34015.","doi":"10.48550/ARXIV.2108.06686","article_processing_charge":"No","department":[{"_id":"GaTk"}],"day":"17","title":"Quantifying the coexistence of neuronal oscillations and avalanches","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_created":"2021-10-04T06:28:32Z","publication":"bioRxiv","oa_version":"Preprint","type":"preprint","main_file_link":[{"url":"https://doi.org/10.1101/2021.09.30.462269","open_access":"1"}],"abstract":[{"lang":"eng","text":"Hippocampal and neocortical neural activity is modulated by the position of the individual in space. While hippocampal neurons provide the basis for a spatial map, prefrontal cortical neurons generalize over environmental features. Whether these generalized representations result from a bidirectional interaction with, or are mainly derived from hippocampal spatial representations is not known. By examining simultaneously recorded hippocampal and medial prefrontal neurons, we observed that prefrontal spatial representations show a delayed coherence with hippocampal ones. We also identified subpopulations of cells in the hippocampus and medial prefrontal cortex that formed functional cross-area couplings; these resembled the optimal connections predicted by a probabilistic model of spatial information transfer and generalization. Moreover, cross-area couplings were strongest and had the shortest delay preceding spatial decision-making. Our results suggest that generalized spatial coding in the medial prefrontal cortex is inherited from spatial representations in the hippocampus, and that the routing of information can change dynamically with behavioral demands."}],"external_id":{"biorxivid":["10.1101/2021.09.30.462269"]},"status":"public","das_tickbox":"1","_id":"10080","date_published":"2021-10-02T00:00:00Z","citation":{"mla":"Nardin, Michele, et al. “The Generalized Spatial Representation in the Prefrontal Cortex Is Inherited from the Hippocampus.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2021.09.30.462269\">10.1101/2021.09.30.462269</a>.","short":"M. Nardin, K. Käfer, J.L. Csicsvari, BioRxiv (n.d.).","apa":"Nardin, M., Käfer, K., &#38; Csicsvari, J. L. (n.d.). The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2021.09.30.462269\">https://doi.org/10.1101/2021.09.30.462269</a>","ista":"Nardin M, Käfer K, Csicsvari JL. The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus. bioRxiv, <a href=\"https://doi.org/10.1101/2021.09.30.462269\">10.1101/2021.09.30.462269</a>.","ama":"Nardin M, Käfer K, Csicsvari JL. The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.09.30.462269\">10.1101/2021.09.30.462269</a>","ieee":"M. Nardin, K. Käfer, and J. L. Csicsvari, “The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus,” <i>bioRxiv</i>. .","chicago":"Nardin, Michele, Karola Käfer, and Jozsef L Csicsvari. “The Generalized Spatial Representation in the Prefrontal Cortex Is Inherited from the Hippocampus.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2021.09.30.462269\">https://doi.org/10.1101/2021.09.30.462269</a>."},"ec_funded":1,"language":[{"iso":"eng"}],"date_updated":"2026-07-29T06:33:53Z","doi":"10.1101/2021.09.30.462269","acknowledgement":"We thank Federico Stella for invaluable suggestions and discussions. We thank Yosman BapatDhar and Andrea Cumpelik for comments, help and suggestions on the exposure of the text. We thank Predrag Živadinović and Juliana Couras for comments on the text and the figures. This work was supported by the EU-FP7 MC-ITN IN-SENS (grant 607616).","project":[{"_id":"257BBB4C-B435-11E9-9278-68D0E5697425","name":"inter-and intracellular signalling in schizophrenia","call_identifier":"FP7","grant_number":"607616"}],"biorxivid":1,"author":[{"full_name":"Nardin, Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8849-6570","first_name":"Michele","last_name":"Nardin"},{"full_name":"Käfer, Karola","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","last_name":"Käfer","first_name":"Karola"},{"full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari"}],"article_processing_charge":"No","year":"2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publication_status":"submitted","title":"The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus","day":"02","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"month":"10"},{"publisher":"Springer Nature","isi":1,"doi":"10.1038/s41598-021-95025-3","acknowledgement":"We thank Alexey Kondrashov, Nick Machnik, Raimundo Julian Saona Urmeneta, Gasper Tkacik and Nick Barton for fruitful discussions. We also thank participants of EvoLunch seminar at IST Austria and the internal seminar at the Banco de España for useful comments. The opinions expressed in this document are exclusively of the authors and, therefore, do not necessarily coincide with those of the Banco de España or the Eurosystem. ETD is supported by the Swiss National Science and Louis Jeantet Foundation. The work of FAK was in part supported by the ERC Consolidator Grant (771209-CharFL).","file":[{"access_level":"open_access","relation":"main_file","creator":"asandaue","content_type":"application/pdf","date_created":"2021-08-16T11:36:49Z","file_size":3432001,"date_updated":"2021-08-16T11:36:49Z","file_id":"9927","file_name":"2021_ScientificReports_Rella.pdf","checksum":"ac86892ed17e6724c7251844da5cef5c","success":1}],"article_number":"15729","quality_controlled":"1","_id":"9905","date_published":"2021-07-30T00:00:00Z","department":[{"_id":"FyKo"}],"day":"30","title":"Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","license":"https://creativecommons.org/licenses/by/4.0/","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["2045-2322"]},"article_processing_charge":"Yes","project":[{"grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020"}],"ddc":["570","610"],"date_updated":"2026-07-29T12:57:49Z","intvolume":"        11","language":[{"iso":"eng"}],"ec_funded":1,"article_type":"original","citation":{"mla":"Rella, Simon, et al. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” <i>Scientific Reports</i>, vol. 11, no. 1, 15729, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41598-021-95025-3\">10.1038/s41598-021-95025-3</a>.","short":"S. Rella, Y.A. Kulikova, E.T. Dermitzakis, F. Kondrashov, Scientific Reports 11 (2021).","apa":"Rella, S., Kulikova, Y. A., Dermitzakis, E. T., &#38; Kondrashov, F. (2021). Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-021-95025-3\">https://doi.org/10.1038/s41598-021-95025-3</a>","ieee":"S. Rella, Y. A. Kulikova, E. T. Dermitzakis, and F. Kondrashov, “Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains,” <i>Scientific Reports</i>, vol. 11, no. 1. Springer Nature, 2021.","ama":"Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. <i>Scientific Reports</i>. 2021;11(1). doi:<a href=\"https://doi.org/10.1038/s41598-021-95025-3\">10.1038/s41598-021-95025-3</a>","ista":"Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. 2021. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. 11(1), 15729.","chicago":"Rella, Simon, Yuliya A. Kulikova, Emmanouil T. Dermitzakis, and Fyodor Kondrashov. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” <i>Scientific Reports</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41598-021-95025-3\">https://doi.org/10.1038/s41598-021-95025-3</a>."},"status":"public","has_accepted_license":"1","external_id":{"pmid":["34330988"],"isi":["000683329100001"]},"abstract":[{"text":"Vaccines are thought to be the best available solution for controlling the ongoing SARS-CoV-2 pandemic. However, the emergence of vaccine-resistant strains may come too rapidly for current vaccine developments to alleviate the health, economic and social consequences of the pandemic. To quantify and characterize the risk of such a scenario, we created a SIR-derived model with initial stochastic dynamics of the vaccine-resistant strain to study the probability of its emergence and establishment. Using parameters realistically resembling SARS-CoV-2 transmission, we model a wave-like pattern of the pandemic and consider the impact of the rate of vaccination and the strength of non-pharmaceutical intervention measures on the probability of emergence of a resistant strain. As expected, we found that a fast rate of vaccination decreases the probability of emergence of a resistant strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions happened at a time when most individuals of the population have already been vaccinated the probability of emergence of a resistant strain was greatly increased. Consequently, we show that a period of transmission reduction close to the end of the vaccination campaign can substantially reduce the probability of resistant strain establishment. Our results suggest that policymakers and individuals should consider maintaining non-pharmaceutical interventions and transmission-reducing behaviours throughout the entire vaccination period.","lang":"eng"}],"type":"journal_article","date_created":"2021-08-15T22:01:26Z","scopus_import":"1","publication":"Scientific Reports","oa_version":"Published Version","month":"07","volume":11,"issue":"1","related_material":{"record":[{"status":"public","id":"20811","relation":"dissertation_contains"}],"link":[{"description":"News on IST Website","relation":"press_release","url":"https://ist.ac.at/en/news/counterintuitive-dynamics-threaten-the-end-of-the-pandemic/"}]},"publication_status":"published","file_date_updated":"2021-08-16T11:36:49Z","year":"2021","pmid":1,"author":[{"last_name":"Rella","first_name":"Simon","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425","full_name":"Rella, Simon"},{"last_name":"Kulikova","first_name":"Yuliya A.","full_name":"Kulikova, Yuliya A."},{"last_name":"Dermitzakis","first_name":"Emmanouil T.","full_name":"Dermitzakis, Emmanouil T."},{"last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor"}]},{"has_accepted_license":"1","status":"public","abstract":[{"lang":"eng","text":"Deep learning is best known for its empirical success across a wide range of applications\r\nspanning computer vision, natural language processing and speech. Of equal significance,\r\nthough perhaps less known, are its ramifications for learning theory: deep networks have\r\nbeen observed to perform surprisingly well in the high-capacity regime, aka the overfitting\r\nor underspecified regime. Classically, this regime on the far right of the bias-variance curve\r\nis associated with poor generalisation; however, recent experiments with deep networks\r\nchallenge this view.\r\n\r\nThis thesis is devoted to investigating various aspects of underspecification in deep learning.\r\nFirst, we argue that deep learning models are underspecified on two levels: a) any given\r\ntraining dataset can be fit by many different functions, and b) any given function can be\r\nexpressed by many different parameter configurations. We refer to the second kind of\r\nunderspecification as parameterisation redundancy and we precisely characterise its extent.\r\nSecond, we characterise the implicit criteria (the inductive bias) that guide learning in the\r\nunderspecified regime. Specifically, we consider a nonlinear but tractable classification\r\nsetting, and show that given the choice, neural networks learn classifiers with a large margin.\r\nThird, we consider learning scenarios where the inductive bias is not by itself sufficient to\r\ndeal with underspecification. We then study different ways of ‘tightening the specification’: i)\r\nIn the setting of representation learning with variational autoencoders, we propose a hand-\r\ncrafted regulariser based on mutual information. ii) In the setting of binary classification, we\r\nconsider soft-label (real-valued) supervision. We derive a generalisation bound for linear\r\nnetworks supervised in this way and verify that soft labels facilitate fast learning. Finally, we\r\nexplore an application of soft-label supervision to the training of multi-exit models."}],"type":"dissertation","corr_author":"1","oa_version":"Published Version","date_created":"2021-05-24T13:06:23Z","language":[{"iso":"eng"}],"citation":{"short":"M. Phuong, Underspecification in Deep Learning, Institute of Science and Technology Austria, 2021.","mla":"Phuong, Mary. <i>Underspecification in Deep Learning</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9418\">10.15479/AT:ISTA:9418</a>.","ieee":"M. Phuong, “Underspecification in deep learning,” Institute of Science and Technology Austria, 2021.","ama":"Phuong M. Underspecification in deep learning. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9418\">10.15479/AT:ISTA:9418</a>","ista":"Phuong M. 2021. Underspecification in deep learning. Institute of Science and Technology Austria.","apa":"Phuong, M. (2021). <i>Underspecification in deep learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9418\">https://doi.org/10.15479/AT:ISTA:9418</a>","chicago":"Phuong, Mary. “Underspecification in Deep Learning.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9418\">https://doi.org/10.15479/AT:ISTA:9418</a>."},"ddc":["000"],"date_updated":"2026-07-30T05:33:52Z","OA_place":"publisher","doi_confirm":"1","author":[{"first_name":"Phuong","last_name":"Bui Thi Mai","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","full_name":"Bui Thi Mai, Phuong"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"},{"_id":"E-Lib"}],"alternative_title":["ISTA Thesis"],"page":"125","publication_status":"published","file_date_updated":"2021-05-24T11:56:02Z","year":"2021","month":"05","related_material":{"record":[{"status":"deleted","id":"7435","relation":"part_of_dissertation"},{"status":"public","id":"7481","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"9416"},{"status":"public","id":"7479","relation":"part_of_dissertation"}]},"supervisor":[{"first_name":"Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}],"date_published":"2021-05-30T00:00:00Z","_id":"9418","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","doi":"10.15479/AT:ISTA:9418","file":[{"checksum":"4f0abe64114cfed264f9d36e8d1197e3","success":1,"date_updated":"2021-05-24T11:22:29Z","file_id":"9419","file_name":"mph-thesis-v519-pdfimages.pdf","file_size":2673905,"date_created":"2021-05-24T11:22:29Z","content_type":"application/pdf","relation":"main_file","creator":"bphuong","access_level":"open_access"},{"content_type":"application/zip","date_created":"2021-05-24T11:56:02Z","creator":"bphuong","relation":"source_file","access_level":"closed","checksum":"f5699e876bc770a9b0df8345a77720a2","file_name":"thesis.zip","file_id":"9420","date_updated":"2021-05-24T11:56:02Z","file_size":92995100}],"publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","title":"Underspecification in deep learning","oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"day":"30"},{"quality_controlled":"1","_id":"9416","date_published":"2021-05-01T00:00:00Z","file":[{"checksum":"f34ff17017527db5ba6927f817bdd125","date_updated":"2021-05-24T11:15:57Z","file_name":"iclr2021_conference.pdf","file_id":"9417","file_size":502356,"content_type":"application/pdf","date_created":"2021-05-24T11:15:57Z","relation":"main_file","creator":"bphuong","access_level":"open_access"}],"conference":{"name":"ICLR: International Conference on Learning Representations","start_date":"2021-05-03","location":"Virtual","end_date":"2021-05-07"},"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"day":"01","title":"The inductive bias of ReLU networks on orthogonally separable data","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"citation":{"chicago":"Phuong, Mary, and Christoph Lampert. “The Inductive Bias of ReLU Networks on Orthogonally Separable Data.” In <i>9th International Conference on Learning Representations</i>, 2021.","apa":"Phuong, M., &#38; Lampert, C. (2021). The inductive bias of ReLU networks on orthogonally separable data. In <i>9th International Conference on Learning Representations</i>. Virtual.","ama":"Phuong M, Lampert C. The inductive bias of ReLU networks on orthogonally separable data. In: <i>9th International Conference on Learning Representations</i>. ; 2021.","ista":"Phuong M, Lampert C. 2021. The inductive bias of ReLU networks on orthogonally separable data. 9th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","ieee":"M. Phuong and C. Lampert, “The inductive bias of ReLU networks on orthogonally separable data,” in <i>9th International Conference on Learning Representations</i>, Virtual, 2021.","mla":"Phuong, Mary, and Christoph Lampert. “The Inductive Bias of ReLU Networks on Orthogonally Separable Data.” <i>9th International Conference on Learning Representations</i>, 2021.","short":"M. Phuong, C. Lampert, in:, 9th International Conference on Learning Representations, 2021."},"has_accepted_license":"1","status":"public","abstract":[{"text":"We study the inductive bias of two-layer ReLU networks trained by gradient flow. We identify a class of easy-to-learn (`orthogonally separable') datasets, and characterise the solution that ReLU networks trained on such datasets converge to. Irrespective of network width, the solution turns out to be a combination of two max-margin classifiers: one corresponding to the positive data subset and one corresponding to the negative data subset. The proof is based on the recently introduced concept of extremal sectors, for which we prove a number of properties in the context of orthogonal separability. In particular, we prove stationarity of activation patterns from some time  onwards, which enables a reduction of the ReLU network to an ensemble of linear subnetworks.","lang":"eng"}],"corr_author":"1","main_file_link":[{"open_access":"1","url":"https://openreview.net/pdf?id=krz7T0xU9Z_"}],"type":"conference","oa_version":"Published Version","date_created":"2021-05-24T11:16:46Z","scopus_import":"1","publication":"9th International Conference on Learning Representations","ddc":["000"],"date_updated":"2026-07-30T05:33:51Z","author":[{"last_name":"Bui Thi Mai","first_name":"Phuong","full_name":"Bui Thi Mai, Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}],"month":"05","related_material":{"record":[{"relation":"dissertation_contains","id":"9418","status":"public"}]},"file_date_updated":"2021-05-24T11:15:57Z","publication_status":"published","year":"2021"},{"year":"2021","publication_status":"published","issue":"3","volume":58,"month":"03","author":[{"first_name":"Naika","last_name":"Meili","full_name":"Meili, Naika"},{"first_name":"Gabriele","last_name":"Manoli","full_name":"Manoli, Gabriele"},{"full_name":"Burlando, Paolo","last_name":"Burlando","first_name":"Paolo"},{"first_name":"Jan","last_name":"Carmeliet","full_name":"Carmeliet, Jan"},{"full_name":"Chow, Winston T.L.","last_name":"Chow","first_name":"Winston T.L."},{"full_name":"Coutts, Andrew M.","first_name":"Andrew M.","last_name":"Coutts"},{"full_name":"Roth, Matthias","first_name":"Matthias","last_name":"Roth"},{"full_name":"Velasco, Erik","last_name":"Velasco","first_name":"Erik"},{"full_name":"Vivoni, Enrique R.","last_name":"Vivoni","first_name":"Enrique R."},{"full_name":"Fatichi, Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","first_name":"Simone","last_name":"Fatichi"}],"OA_place":"publisher","intvolume":"        58","date_updated":"2026-07-30T08:40:12Z","ddc":["550"],"OA_type":"hybrid","date_created":"2026-07-27T12:30:23Z","scopus_import":"1","oa_version":"Published Version","publication":"Urban Forestry & Urban Greening","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.ufug.2020.126970"}],"abstract":[{"text":"Increasing urban tree cover is an often proposed mitigation strategy against urban heat as trees are expected to cool cities through evapotranspiration and shade provision. However, trees also modify wind flow and urban aerodynamic roughness, which can potentially limit heat dissipation. Existing studies show a varying cooling potential of urban trees in different climates and times of the day. These differences are so far not systematically explained as partitioning the individual tree effects is challenging and impossible through observations alone. Here, we conduct numerical experiments removing and adding radiation, evapotranspiration, and aerodynamic roughness effects caused by urban trees using a mechanistic urban ecohydrological model. Simulations are presented for four cities in different climates (Phoenix, Singapore, Melbourne, Zurich) considering the seasonal and diurnal cycles of air and surface temperatures.\r\nResults show that evapotranspiration of well-watered trees alone can decrease local 2 m air temperature at maximum by 3.1– 5.8 °C in the four climates during summer. Further cooling is prevented by stomatal closure at peak temperatures as high vapour pressure deficits limit transpiration. While shading reduces surface temperatures, the interaction of a non-transpiring tree with radiation can increase 2 m air temperature by up to 1.6 – 2.1 °C in certain hours of the day at local scale, thus partially counteracting the evapotranspirative cooling effect. Furthermore, in the analysed scenarios, which do not account for tree wind blockage effects, trees lead to a decrease in urban roughness, which inhibits turbulent energy exchange and increases air temperature during daytime. At night, single tree effects are variable likely due to differences in atmospheric stability within the urban canyon. These results explain reported diurnal, seasonal and climatic differences in the cooling effects of urban trees, and can guide future field campaigns, planning strategies, and species selection aimed at improving local microclimate using urban greenery.","lang":"eng"}],"has_accepted_license":"1","status":"public","article_type":"original","citation":{"chicago":"Meili, Naika, Gabriele Manoli, Paolo Burlando, Jan Carmeliet, Winston T.L. Chow, Andrew M. Coutts, Matthias Roth, Erik Velasco, Enrique R. Vivoni, and Simone Fatichi. “Tree Effects on Urban Microclimate: Diurnal, Seasonal, and Climatic Temperature Differences Explained by Separating Radiation, Evapotranspiration, and Roughness Effects.” <i>Urban Forestry &#38; Urban Greening</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.ufug.2020.126970\">https://doi.org/10.1016/j.ufug.2020.126970</a>.","apa":"Meili, N., Manoli, G., Burlando, P., Carmeliet, J., Chow, W. T. L., Coutts, A. M., … Fatichi, S. (2021). Tree effects on urban microclimate: Diurnal, seasonal, and climatic temperature differences explained by separating radiation, evapotranspiration, and roughness effects. <i>Urban Forestry &#38; Urban Greening</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ufug.2020.126970\">https://doi.org/10.1016/j.ufug.2020.126970</a>","ama":"Meili N, Manoli G, Burlando P, et al. Tree effects on urban microclimate: Diurnal, seasonal, and climatic temperature differences explained by separating radiation, evapotranspiration, and roughness effects. <i>Urban Forestry &#38; Urban Greening</i>. 2021;58(3). doi:<a href=\"https://doi.org/10.1016/j.ufug.2020.126970\">10.1016/j.ufug.2020.126970</a>","ieee":"N. Meili <i>et al.</i>, “Tree effects on urban microclimate: Diurnal, seasonal, and climatic temperature differences explained by separating radiation, evapotranspiration, and roughness effects,” <i>Urban Forestry &#38; Urban Greening</i>, vol. 58, no. 3. Elsevier, 2021.","ista":"Meili N, Manoli G, Burlando P, Carmeliet J, Chow WTL, Coutts AM, Roth M, Velasco E, Vivoni ER, Fatichi S. 2021. Tree effects on urban microclimate: Diurnal, seasonal, and climatic temperature differences explained by separating radiation, evapotranspiration, and roughness effects. Urban Forestry &#38; Urban Greening. 58(3), 126970.","mla":"Meili, Naika, et al. “Tree Effects on Urban Microclimate: Diurnal, Seasonal, and Climatic Temperature Differences Explained by Separating Radiation, Evapotranspiration, and Roughness Effects.” <i>Urban Forestry &#38; Urban Greening</i>, vol. 58, no. 3, 126970, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.ufug.2020.126970\">10.1016/j.ufug.2020.126970</a>.","short":"N. Meili, G. Manoli, P. Burlando, J. Carmeliet, W.T.L. Chow, A.M. Coutts, M. Roth, E. Velasco, E.R. Vivoni, S. Fatichi, Urban Forestry &#38; Urban Greening 58 (2021)."},"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Tree effects on urban microclimate: Diurnal, seasonal, and climatic temperature differences explained by separating radiation, evapotranspiration, and roughness effects","day":"01","article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"eissn":["1610-8167"],"issn":["1618-8667"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"extern":"1","doi":"10.1016/j.ufug.2020.126970","publisher":"Elsevier","das_tickbox":"1","date_published":"2021-03-01T00:00:00Z","_id":"22472","quality_controlled":"1","article_number":"126970"},{"author":[{"first_name":"Muhammad Omer","last_name":"Mughal","full_name":"Mughal, Muhammad Omer"},{"last_name":"Kubilay","first_name":"Aytac","full_name":"Kubilay, Aytac"},{"full_name":"Fatichi, Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","last_name":"Fatichi","first_name":"Simone"},{"last_name":"Meili","first_name":"Naika","full_name":"Meili, Naika"},{"full_name":"Carmeliet, Jan","last_name":"Carmeliet","first_name":"Jan"},{"last_name":"Edwards","first_name":"Peter","full_name":"Edwards, Peter"},{"first_name":"Paolo","last_name":"Burlando","full_name":"Burlando, Paolo"}],"publication_status":"published","year":"2021","month":"09","volume":39,"abstract":[{"text":"In light of globally increasing temperatures, accentuated in cities by the urban heat island effect, urban planners and designers are looking for new, quantitative methods to assess the performance of their designs in terms of ecosystem services provided by vegetation. Among these ecosystem services, improved microclimate conditions are particularly important for human thermal comfort and health. In this study, an urban scene in the tropical city of Singapore is numerically investigated with a fully-integrated, three-dimensional urban microclimate model implemented in OpenFOAM. Mass and heat transport in air and storage effect in the urban environment are coupled so that the daily turbulent transport in air using steady Reynolds-averaged Navier-Stokes (RANS) can be solved iteratively with the unsteady heat and moisture transfer from urban surfaces. Vegetation is modeled as a porous medium for the flow of moist air and a leaf energy balance model is used to determine the heat fluxes and transpiration at leaf surfaces. The analysis shows the influence of an urban park upon air temperatures and thermal comfort. Cooling intensity of 1 °C is observed downwind of the park within a region of 27 m for an incoming wind speed of 2.3 m s−1, which reduces to 0.6 °C at a distance of 117 m from the park. The Universal Thermal Comfort Index (UTCI) shows a reduction in thermal stress in and around the park. The approach presented here can provide specific guidelines for urban planners and frame expectations on magnitude and spatial extent of local microclimate modifications generated by an urban park in a tropical city.","lang":"eng"}],"has_accepted_license":"1","status":"public","date_created":"2026-07-27T12:30:23Z","oa_version":"Published Version","scopus_import":"1","publication":"Urban Climate","main_file_link":[{"url":"https://doi.org/10.1016/j.uclim.2021.100939","open_access":"1"}],"type":"journal_article","article_type":"original","citation":{"chicago":"Mughal, Muhammad Omer, Aytac Kubilay, Simone Fatichi, Naika Meili, Jan Carmeliet, Peter Edwards, and Paolo Burlando. “Detailed Investigation of Vegetation Effects on Microclimate by Means of Computational Fluid Dynamics (CFD) in a Tropical Urban Environment.” <i>Urban Climate</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.uclim.2021.100939\">https://doi.org/10.1016/j.uclim.2021.100939</a>.","mla":"Mughal, Muhammad Omer, et al. “Detailed Investigation of Vegetation Effects on Microclimate by Means of Computational Fluid Dynamics (CFD) in a Tropical Urban Environment.” <i>Urban Climate</i>, vol. 39, 100939, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.uclim.2021.100939\">10.1016/j.uclim.2021.100939</a>.","short":"M.O. Mughal, A. Kubilay, S. Fatichi, N. Meili, J. Carmeliet, P. Edwards, P. Burlando, Urban Climate 39 (2021).","apa":"Mughal, M. O., Kubilay, A., Fatichi, S., Meili, N., Carmeliet, J., Edwards, P., &#38; Burlando, P. (2021). Detailed investigation of vegetation effects on microclimate by means of computational fluid dynamics (CFD) in a tropical urban environment. <i>Urban Climate</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.uclim.2021.100939\">https://doi.org/10.1016/j.uclim.2021.100939</a>","ieee":"M. O. Mughal <i>et al.</i>, “Detailed investigation of vegetation effects on microclimate by means of computational fluid dynamics (CFD) in a tropical urban environment,” <i>Urban Climate</i>, vol. 39. Elsevier, 2021.","ista":"Mughal MO, Kubilay A, Fatichi S, Meili N, Carmeliet J, Edwards P, Burlando P. 2021. Detailed investigation of vegetation effects on microclimate by means of computational fluid dynamics (CFD) in a tropical urban environment. Urban Climate. 39, 100939.","ama":"Mughal MO, Kubilay A, Fatichi S, et al. Detailed investigation of vegetation effects on microclimate by means of computational fluid dynamics (CFD) in a tropical urban environment. <i>Urban Climate</i>. 2021;39. doi:<a href=\"https://doi.org/10.1016/j.uclim.2021.100939\">10.1016/j.uclim.2021.100939</a>"},"language":[{"iso":"eng"}],"date_updated":"2026-07-30T09:08:16Z","ddc":["550"],"OA_place":"publisher","intvolume":"        39","OA_type":"hybrid","publication_identifier":{"eissn":["2212-0955"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","oa":1,"title":"Detailed investigation of vegetation effects on microclimate by means of computational fluid dynamics (CFD) in a tropical urban environment","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","das_tickbox":"1","article_number":"100939","_id":"22474","date_published":"2021-09-01T00:00:00Z","quality_controlled":"1","extern":"1","publisher":"Elsevier","doi":"10.1016/j.uclim.2021.100939"},{"citation":{"mla":"Martinetti, Stefano, et al. “Field Evidence of Riparian Vegetation Response to Groundwater Levels in a Gravel‐bed River.” <i>Ecohydrology</i>, vol. 14, no. 2, e2264, Wiley, 2021, doi:<a href=\"https://doi.org/10.1002/eco.2264\">10.1002/eco.2264</a>.","short":"S. Martinetti, S. Fatichi, M. Floriancic, P. Burlando, P. Molnar, Ecohydrology 14 (2021).","apa":"Martinetti, S., Fatichi, S., Floriancic, M., Burlando, P., &#38; Molnar, P. (2021). Field evidence of riparian vegetation response to groundwater levels in a gravel‐bed river. <i>Ecohydrology</i>. Wiley. <a href=\"https://doi.org/10.1002/eco.2264\">https://doi.org/10.1002/eco.2264</a>","ama":"Martinetti S, Fatichi S, Floriancic M, Burlando P, Molnar P. Field evidence of riparian vegetation response to groundwater levels in a gravel‐bed river. <i>Ecohydrology</i>. 2021;14(2). doi:<a href=\"https://doi.org/10.1002/eco.2264\">10.1002/eco.2264</a>","ieee":"S. Martinetti, S. Fatichi, M. Floriancic, P. Burlando, and P. Molnar, “Field evidence of riparian vegetation response to groundwater levels in a gravel‐bed river,” <i>Ecohydrology</i>, vol. 14, no. 2. Wiley, 2021.","ista":"Martinetti S, Fatichi S, Floriancic M, Burlando P, Molnar P. 2021. Field evidence of riparian vegetation response to groundwater levels in a gravel‐bed river. Ecohydrology. 14(2), e2264.","chicago":"Martinetti, Stefano, Simone Fatichi, Marius Floriancic, Paolo Burlando, and Peter Molnar. “Field Evidence of Riparian Vegetation Response to Groundwater Levels in a Gravel‐bed River.” <i>Ecohydrology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/eco.2264\">https://doi.org/10.1002/eco.2264</a>."},"article_type":"original","language":[{"iso":"eng"}],"publication":"Ecohydrology","oa_version":"None","date_created":"2026-07-27T12:30:23Z","scopus_import":"1","type":"journal_article","abstract":[{"text":"Vegetation establishment, growth and succession in riparian ecosystems are linked to river flow dynamics and groundwater table fluctuations. This is especially true in Alpine gravel-bed rivers with wide floodplains, geomorphically active floods and a strong river-aquifer exchange. The role of short-term groundwater fluctuations is not always clear in these ecosystems, as it is assumed that phreatophytic vegetation close to rivers is adapted to such conditions. Here, we provide data evidence of riparian plant response to short-term groundwater table fluctuations in a braided gravel-bed river (Maggia). We used indirect physiological variables for photosynthesis and transpiration—stomatal conductance gs and daily variation in stem diameter ΔDd—which we measured at six mature riparian trees of the Salicaceae family at two sites with different mean depths to groundwater during two growing seasons. The data demonstrate that (a) short-term variation of the groundwater table affects riparian vegetation—at the site with deeper groundwater, the water table depth was the best predictor of gs variability, while at the site with shallower groundwater, temperature and vapour pressure deficit (VPD) were the best predictors of ΔDd variability; (b) instantaneous stomatal conductance is related to VPD, but conditioned by groundwater levels, with higher stomatal conductance for the same radiative input and VPD when the water table was higher for all trees; and (c) local microclimate measured at tree locations had a stronger predictive power for gs than valley scale climate, suggesting local climate controls on vegetated stands on gravel bars. Our results provide evidence of riparian trees undertaking physiological adjustments to transpiration in response to groundwater stage, depending on their riparian floodplain setting.","lang":"eng"}],"status":"public","OA_type":"closed access","intvolume":"        14","date_updated":"2026-07-30T08:46:20Z","author":[{"first_name":"Stefano","last_name":"Martinetti","full_name":"Martinetti, Stefano"},{"last_name":"Fatichi","first_name":"Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","full_name":"Fatichi, Simone"},{"full_name":"Floriancic, Marius","first_name":"Marius","last_name":"Floriancic"},{"last_name":"Burlando","first_name":"Paolo","full_name":"Burlando, Paolo"},{"first_name":"Peter","last_name":"Molnar","full_name":"Molnar, Peter"}],"issue":"2","volume":14,"month":"03","year":"2021","publication_status":"published","date_published":"2021-03-01T00:00:00Z","_id":"22468","quality_controlled":"1","article_number":"e2264","das_tickbox":"1","doi":"10.1002/eco.2264","publisher":"Wiley","extern":"1","article_processing_charge":"No","publication_identifier":{"issn":["1936-0584"],"eissn":["1936-0592"]},"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Field evidence of riparian vegetation response to groundwater levels in a gravel‐bed river"}]